sry for my probably simple question, but i got some serious problem with a certain BLAST query.
I searching for the best spots to place two opposing zinc finger nucleases in a certain gene.
Screening for the very sequences is done by ZiFiT, no problem.
The first nine nucleotids are for the first protein, then a spacer and the second protein.
Now I need to get sure, that there a few as possible other sequences in the whole genome that are the same or similiar.
I need the two nucleases be as specific as possible.
Therefore I blast the sequence.
Since these proteins need to dimerize to work, I don't care, if the first part or the second part of the sequence happen to be somewhere else isolated too.
I'm only interested if both parts, with the proper spacer in between, happen to be somewhere else too, or similiar sequences respectively.
Now blastn gives me both results.
It gives me the one I'm interested in, like that:
Score = 23.8 bits (12), Expect = 2498
Identities = 18/24 (75%), Gaps = 0/24 (0%)
Query 1 CGCGACCCCNNNNNNGGCGCGGCC 24
Sbjct 93104646 CGCGACCCCGTCCCGGGCGCGGCC 93104669
but it also gives me the short ones, i'm not interested in, like that:
Score = 18.0 bits (9), Expect = 136135
Identities = 9/9 (100%), Gaps = 0/9 (0%)
Query 16 GGCGCGGCC 24
Sbjct 1800501 GGCGCGGCC 1800493
So, basically what I need, is how to restrict the results to a certain lenght, I guess (not to a certain minimum amount of identity, but just to a minimum amount of length as a wohle).
Again, sry for my simple question, but I tried a lot, and just haven't come to an end yet.
It would be awesome if someone could give me a hint how to do that.